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update removal to remove all non-autosomal chromosomes
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sof202 committed Apr 12, 2024
1 parent ee60f8f commit 24f0496
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions JobSubmission/4_BinarizeBamFiles.sh
Original file line number Diff line number Diff line change
Expand Up @@ -276,9 +276,10 @@ rm -r "${BINARY_DIR}/BinSize_${bin_size}_SampleSize_${sample_size}/bed"

# Non-autosomal chromosomes are not factored into ldsc step of the pipeline
# so we minimise their impact by deleting their associated binary files
find . \
find "${BINARY_DIR}/BinSize_${bin_size}_SampleSize_${sample_size}" \
-type f \
-regex '^[a-zA-Z\._\/]+$' \
! -name "ChromOptimise_chr[0-9]_binary.txt.gz" \
-a ! -name "ChromOptimise_chr[0-9][0-9]_binary.txt.gz" \
-exec rm {} \;

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